You can use olinks right now. One of the most frequent uses of olinks
is for linking between modular content. Olinks let you avoid hard coding
filenames in your links, which can be troublesome to maintain if you
rename or move files.
Do you mean using OLinks without targetdoc attributes to avoid ID/IDREFs
warning when editing standalone modules or do you have any idea how
OLink database should relate to assembly structure and what should be
separate OLink target document from assembly point of view?
Although there are many benefits of OLinks I think that assembly should
also provide linking similar to one known from DITA which allows direct
linking to source XML file of module.